Nucleic acid hybridization is an important technique for detecting the presence of particular sequence information. Recent advances have allowed for the production of high density oligonucleotide arrays which may have great utility for research and clinical diagnostics. Typically, a sequence is amplified and labeled with fluorescent tags. The sample is incubated with the probe array and the sample is washed with a series of increasingly stringent buffers. Stringency may be provided by means of reduced salt concentration or increased temperature. Reduced salt concentrations lead to electrostatic repulsion between phosphate groups, thereby lowering the melting temperature (T.sub.m).
The number of different sequences on each array is ultimately limited by the detection capabilities of the instrument analyzing it and factors such as contaminating fluorescent compounds, stray light, and hybridization of mismatched oligonucleotides. As the stringency of hybridization is increased, the noise level from mismatches is reduced (increasing specificity), but the overall signal is also reduced due to loss of correctly hybridized molecules (decreasing sensitivity).
Two related and important amplification techniques which depend on the specificity and sensitivity of oligonucleotide hybridization are polymerase chain reaction (PCR) and ligase chain reaction (LCR), which are commonly used in medical diagnostics and research.